Research workbench
Vx-inhibited acetylcholinesterase in complex with 2-((hydroxyimino) methyl)-1-(5-(4-methyl-3-NITROBENZAMIDO)PENTYL)PYRIDINIUM
Analyse Vx-inhibited acetylcholinesterase in complex with 2-((hydroxyimino)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R3C
- Type
- protein
- Length
- 1,067 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholinesterase
- EC
- 3.1.1.7
- UniProt
- P21836
- Ligands
- TOE, I1X, P15, NAG
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholinesterase (EC 3.1.1.7) | protein | 535 | 39% helix, 18% strand | P21836 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 532 | 38% helix, 18% strand | P21836 |
Ligands and binding sites
- TOE · 2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxyl · ligand · 3 copies · chains A, B
- I1X · 4-methyl-3-nitro-~{N}-[(2~{E},4~{E})-5-[2-[(oxidanylamino)methyl]pyridin-1-yl]penta-2,4-dienyl]benzamide · ligand · 2 copies · chains A, B
- P15 · 2,5,8,11,14,17-hexaoxanonadecan-19-ol · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.74 | 0.89 | 35 | I1X |
| 2 | 195 | 0.72 | 0.89 | 34 | I1X |
| 3 | 304 | 0.64 | 0.80 | 44 | PG0, P15, TOE |
| 4 | 398 | 0.63 | 0.78 | 37 | empty |
| 5 | 186 | 0.59 | 0.82 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 967 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P21836
- Elsewhere: RCSB PDB 7R3C · PDBe 7R3C · UniProt P21836
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